--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/KCountArray3.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,155 @@
+package bloom;
+
+/**
+ * @author Brian Bushnell
+ * @date Aug 17, 2012
+ *
+ */
+public class KCountArray3 extends KCountArray {
+		
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -5466091642729698944L;
+	
+	public KCountArray3(long cells_, int bits_){
+		super(cells_, bits_);
+		long words=cells/cellsPerWord;
+		int wordsPerArray=(int)(words/numArrays);
+		matrix=new int[numArrays][wordsPerArray];
+	}
+	
+	@Override
+	public int read(long key){
+		if(verbose){System.err.println("Reading "+key);}
+//		System.out.println("key="+key);
+		int arrayNum=(int)(key&arrayMask);
+//		System.out.println("array="+arrayNum);
+		key>>>=arrayBits;
+//		System.out.println("key2="+key);
+		int[] array=matrix[arrayNum];
+		int index=(int)(key>>>indexShift);
+//		System.out.println("index="+index);
+		int word=array[index];
+//		System.out.println("word="+Integer.toHexString(word));
+		int cellShift=(int)(cellBits*key);
+//		System.out.println("cellShift="+cellShift);
+		int value=(int)((word>>>cellShift)&valueMask);
+		if(verbose){System.err.println("Read "+value);}
+		return value;
+	}
+	
+	@Override
+	public void write(long key, int value){
+		if(verbose){System.err.println("Writing "+key+", "+value);}
+		int arrayNum=(int)(key&arrayMask);
+		key>>>=arrayBits;
+		int[] array=matrix[arrayNum];
+		int index=(int)(key>>>indexShift);
+		int word=array[index];
+		int cellShift=(int)(cellBits*key);
+		word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
+		array[index]=word;
+	}
+	
+//	static int count138=0;
+	@Override
+	public void increment(long key, int incr){
+		if(verbose){System.err.println("*** Incrementing "+key);}
+//		if(key==138){
+//			assert(count138==0) : count138;
+//			count138++;
+//		}
+		int arrayNum=(int)(key&arrayMask);
+		key>>>=arrayBits;
+		int[] array=matrix[arrayNum];
+		int index=(int)(key>>>indexShift);
+		int word=array[index];
+		int cellShift=(int)(cellBits*key);
+		int value=((word>>>cellShift)&valueMask);
+		if(value==0 && incr>0){cellsUsed++;}
+		else if(incr<0 && value+incr==0){cellsUsed--;}
+		value=min(value+incr, maxValue);
+		word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
+		array[index]=word;
+		if(verbose){System.err.println("Returning "+value);}
+		//return (int)value;
+	}
+	
+	/** Returns unincremented value */
+	@Override
+	public int incrementAndReturnUnincremented(long key, int incr){
+		if(verbose){System.err.println("Incrementing2 "+key);}
+		int arrayNum=(int)(key&arrayMask);
+		key>>>=arrayBits;
+		int[] array=matrix[arrayNum];
+		int index=(int)(key>>>indexShift);
+		int word=array[index];
+		int cellShift=(int)(cellBits*key);
+		final int value=((word>>>cellShift)&valueMask);
+		final int value2=min(value+incr, maxValue);
+		word=(value2<<cellShift)|(word&~((valueMask)<<cellShift));
+		array[index]=word;
+		if(verbose){System.err.println("Returning "+value);}
+		return value;
+	}
+	
+	@Override
+	public long[] transformToFrequency(){
+		return transformToFrequency(matrix);
+	}
+	
+	@Override
+	public String toContentsString(){
+		StringBuilder sb=new StringBuilder();
+		sb.append("[");
+		String comma="";
+		for(int[] array : matrix){
+			for(int i=0; i<array.length; i++){
+				int word=array[i];
+				for(int j=0; j<cellsPerWord; j++){
+					int x=word&valueMask;
+					sb.append(comma);
+					sb.append(x);
+					word>>>=cellBits;
+					comma=", ";
+				}
+			}
+		}
+		sb.append("]");
+		return sb.toString();
+	}
+	
+	@Override
+	public double usedFraction(){return cellsUsed/(double)cells;}
+	
+	@Override
+	public double usedFraction(int mindepth){return cellsUsed(mindepth)/(double)cells;}
+	
+	@Override
+	public long cellsUsed(int mindepth){
+		long count=0;
+		for(int[] array : matrix){
+			if(array!=null){
+				for(int word : array){
+					while(word>0){
+						int x=word&valueMask;
+						if(x>=mindepth){count++;}
+						word>>>=cellBits;
+					}
+				}
+			}
+		}
+		return count;
+	}
+	
+	@Override
+	long hash(long x, int y) {
+		assert(false) : "Unsupported.";
+		return x;
+	}
+	
+	private long cellsUsed;
+	private final int[][] matrix;
+	
+}